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#
# test/unit/bio/db/test_soft.rb - Unit test for Bio::SOFT
#
# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
# License:: The Ruby License
#
# $Id:$
#
# loading helper routine for testing bioruby
require 'pathname'
load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3,
'bioruby_test_helper.rb')).cleanpath.to_s
# libraries needed for the tests
require 'test/unit'
require 'bio/db/soft'
module Bio #:nodoc:
class TestSOFT < Test::Unit::TestCase #:nodoc:
def setup
test_data_path = Pathname.new(File.join(BioRubyTestDataPath, 'soft')).cleanpath.to_s
series_filename = File.join(test_data_path, 'GSE3457_family_partial.soft')
dataset_filename = File.join(test_data_path, 'GDS100_partial.soft')
@obj_series = Bio::SOFT.new( IO.readlines(series_filename))
@obj_dataset = Bio::SOFT.new( IO.readlines(dataset_filename))
end
def test_series
assert_equal( @obj_series.platform[:geo_accession], 'GPL2092')
assert_equal( @obj_series.platform[:organism], 'Populus')
assert_equal( @obj_series.platform[:contributor], ["Jingyi,,Li", "Olga,,Shevchenko", "Steve,H,Strauss", "Amy,M,Brunner"])
assert_equal( @obj_series.platform[:data_row_count], '240')
assert_equal( @obj_series.platform.keys.sort {|a,b| a.to_s <=> b.to_s}[0..2], [:contact_address, :contact_city, :contact_country])
assert_equal( @obj_series.platform[:"contact_zip/postal_code"], '97331')
assert_equal( @obj_series.platform[:table].header, ["ID", "GB_ACC", "SPOT_ID", "Function/Family", "ORGANISM", "SEQUENCE"])
assert_equal( @obj_series.platform[:table].header_description, {"ORGANISM"=>"sequence sources",
"SEQUENCE"=>"oligo sequence used",
"Function/Family"=>"gene functions and family",
"ID"=>"",
"SPOT_ID"=>"",
"GB_ACC"=>"Gene bank accession number"})
assert_equal( @obj_series.platform[:table].rows.size, 240)
assert_equal( @obj_series.platform[:table].rows[5], ["A039P68U",
"AI163321",
"",
"TF, flowering protein CONSTANS",
"P. tremula x P. tremuloides",
"AGAAAATTCGATATACTGTCCGTAAAGAGGTAGCACTTAGAATGCAACGGAATAAAGGGCAGTTCACCTC"])
assert_equal( @obj_series.platform[:table].rows[5][4], 'P. tremula x P. tremuloides')
assert_equal( @obj_series.platform[:table].rows[5][:organism], 'P. tremula x P. tremuloides')
assert_equal( @obj_series.platform[:table].rows[5]['ORGANISM'], 'P. tremula x P. tremuloides')
assert_equal( @obj_series.series[:geo_accession], 'GSE3457')
assert_equal( @obj_series.series[:contributor], ["Jingyi,,Li",
"Olga,,Shevchenko",
"Ove,,Nilsson",
"Steve,H,Strauss",
"Amy,M,Brunner"])
assert_equal( @obj_series.series[:platform_id], 'GPL2092')
assert_equal( @obj_series.series[:sample_id].size, 74)
assert_equal( @obj_series.series[:sample_id][0..4], ["GSM77557", "GSM77558", "GSM77559", "GSM77560", "GSM77561"])
assert_equal( @obj_series.database[:name], 'Gene Expression Omnibus (GEO)')
assert_equal( @obj_series.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')
assert_equal( @obj_series.database[:institute], 'NCBI NLM NIH')
assert_equal( @obj_series.samples.size, 2)
assert_equal( @obj_series.samples[:GSM77557][:series_id], 'GSE3457')
assert_equal( @obj_series.samples['GSM77557'][:series_id], 'GSE3457')
assert_equal( @obj_series.samples[:GSM77557][:platform_id], 'GPL2092')
assert_equal( @obj_series.samples[:GSM77557][:type], 'RNA')
assert_equal( @obj_series.samples[:GSM77557][:title], 'fb6a1')
assert_equal( @obj_series.samples[:GSM77557][:table].header, ["ID_REF", "VALUE"])
assert_equal( @obj_series.samples[:GSM77557][:table].header_description, {"ID_REF"=>"", "VALUE"=>"normalized signal intensities"})
assert_equal( @obj_series.samples[:GSM77557][:table].rows.size, 217)
assert_equal( @obj_series.samples[:GSM77557][:table].rows[5], ["A039P68U", "5.36"])
assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][0], 'A039P68U')
assert_equal( @obj_series.samples[:GSM77557][:table].rows[5][:id_ref], 'A039P68U')
assert_equal( @obj_series.samples[:GSM77557][:table].rows[5]['ID_REF'], 'A039P68U')
end
def test_dataset
assert_equal( @obj_dataset.database[:name], 'Gene Expression Omnibus (GEO)')
assert_equal( @obj_dataset.database[:ref], 'Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6')
assert_equal( @obj_dataset.database[:institute], 'NCBI NLM NIH')
assert_equal( @obj_dataset.subsets.size, 8)
assert_equal( @obj_dataset.subsets.keys.sort, ["GDS100_1",
"GDS100_2",
"GDS100_3",
"GDS100_4",
"GDS100_5",
"GDS100_6",
"GDS100_7",
"GDS100_8"])
assert_equal( @obj_dataset.subsets[:GDS100_7], {:sample_id=>"GSM548,GSM543",
:dataset_id=>"GDS100",
:description=>"60 minute",
:type=>"time"})
assert_equal( @obj_dataset.subsets['GDS100_7'][:sample_id], 'GSM548,GSM543')
assert_equal( @obj_dataset.subsets[:GDS100_7][:sample_id], 'GSM548,GSM543')
assert_equal( @obj_dataset.subsets[:GDS100_7][:dataset_id], 'GDS100')
assert_equal( @obj_dataset.dataset[:order], 'none')
assert_equal( @obj_dataset.dataset[:sample_organism], 'Escherichia coli')
assert_equal( @obj_dataset.dataset[:table].header, ["ID_REF",
"IDENTIFIER",
"GSM549",
"GSM542",
"GSM543",
"GSM547",
"GSM544",
"GSM545",
"GSM546",
"GSM548"])
assert_equal( @obj_dataset.dataset[:table].rows.size, 15)
assert_equal( @obj_dataset.dataset[:table].rows[5], ["6",
"EMPTY",
"0.097",
"0.217",
"0.242",
"0.067",
"0.104",
"0.162",
"0.104",
"0.154"])
assert_equal( @obj_dataset.dataset[:table].rows[5][4], '0.242')
assert_equal( @obj_dataset.dataset[:table].rows[5][:gsm549], '0.097')
assert_equal( @obj_dataset.dataset[:table].rows[5][:GSM549], '0.097')
assert_equal( @obj_dataset.dataset[:table].rows[5]['GSM549'], '0.097')
end
end
end
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